Additional file 2 of LAST-seq: single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesis

Additional file 2: Table S1. gDNA contamination test. Table S2. Oligos of short IVT templates; primers for long template construction and IVT quantification; primer for SCC4 knockout. Table S3. LAST-seq barcoding primers and library indexing primers. Table S4. Primers for A60 spike-ins. Table S5. Quantification of A60 spike-ins

Additional file 1 of LAST-seq: single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesis

Additional file 1: Fig. S1. Simulated performance of scRNA-seq with varying single-molecule capture efficiency. Fig. S2. T7 In vitro transcription (IVT) of ssRNA templates. Fig. S3. LAST-seq primer. Fig. S4. Performance of LAST-seq and comparison to SMART-seq. Fig. S5. Comparison between LAST-seq and CEL-seq. Fig. S6. Transcriptional bursting kinetics in human cells. Fig. S7. Chromatin structure and gene expression level in wildtype and SCC4 knockout haploid human cells. Fig. S8. LAST-seq library

Additional file 3 of LAST-seq: single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesis

Additional file 3. Review history

GSEA analysis of the differentially expressed mRNA.

GSEA analysis of the differentially expressed mRNA.</p

DataSheet2_Prognostic Implications of Pyroptosis-Related Gene Signatures in Lung Squamous Cell Carcinoma.ZIP

Background: Lung squamous cell carcinoma (LUSC) has been a highly malignant tumor with very poor prognosis. It is confirmed that pyroptosis refers to the deaths of cells in a programmed and inflammatory manner. Nevertheless, the correlation between expression of genes related with pyroptosis and their prognosis remains uncertain in LUSC.Methods: Utilization of The Cancer Genome Atlas (TCGA) cohort has been done for evaluating the prognostics of pyroptosis-related genes for survival and constructing a signature with multiple genes. The least absolute shrinkage and selection operator (LASSO) Cox regression was performed for establishing such pyroptosis-related gene signature.Results: Eventually, identification of 28 genes in relation to pyroptosis was made in LUSC and healthy lung tissues. Upon the basis of these differentially-expressed genes (DEGs), the patients of LUSC can be divided into two subtypes. Nine gene signatures were established using LASSO. The surviving rate for low-risk group was apparently greater in contrast with the high-risk group (p Conclusion: Genes in relation with pyroptosis played an essential role in tumor immunity, which is capable of predicting the prognosis for LUSCs.</p

The differently expressed miRNAs in TCGA.

(XLS)</p

PPI network of LUSC related target genes.

PPI network of LUSC related target genes.</p

Potential association between microRNA and target genes.

Red dot indicates upregulated, and green dot means downregulated.</p

The results of GO analysis and KEGG analysis of target genes.

(XLS)</p

Online databases to predicted 99 target genes of these seven miRNAs.

(XLS)</p